Saturday, September 29, 2007

The enigmatic Hobbit is in the news again. About a week ago National Public Radio website which has a pretty solid reputation for good science reporting carried this headline, "Case Grows for 'Hobbit' as Human Ancestor". First some background. Remains of a 3 feet tall human-like creature, technically know as Homo floresiensis, with a brain much smaller than modern humans, were discovered on the island of Flores in Indonesia in 2004. The remains range in age from about 20 -12 thousand years old. Controversy has raged on whether this creature nicknamed the Hobbit represents an extinct species of the human family or whether the remains are of pygmy modern humans (Homo sapiens) with a rare genetic condition known as microcephaly, which causes retardation of brain growth among other body deformities. You can follow the controversy in this series of blogs. The balance of evidence seems to be favoring the hypothesis that Homo floresiensis is a different species of hominid. The latest research dealt with shape of wrist bones, which according to researchers are not at all like the wrist bones in modern humans and Neanderthals, but more like wrist bones in early Homo erectus, the species considered ancestral to modern humans.

So, assuming that the Hobbit is a different species, does that justify a headline calling it a human ancestor? Image below shows the family tree of hominids, showing not only the pattern of branching but also the geographic distribution of the various hominid species.

Note: I just cannot remember where I downloaded this image. If anyone recognizes the source do let me know and I will credit it.

There is still a lot of disagreement on the status of Homo erectus. Some anthropologists call remains of early Homo found in Asia by the species name erectus, preferring the name ergaster for African representatives of early genus Homo. Others prefer naming all early Homo as erectus, a convention I will use here for the purpose of this discussion. What do we make of the early evolution and diversification of Homo erectus? It is convenient to think of erectus as a group of interbreeding populations living in East Africa about 1.2 million years ago. At some point after this date, some members of this population migrated to Indonesia and settled there. Some generations later, some more members of the population in East Africa, left for Europe and settled there. The rest of the population stayed in Africa. The three branches did not have any contact with each other thereafter. Homo floresiensis, Neanderthals and modern humans are the descendants of the populations which settled in Indonesia, Europe and east Africa respectively. That makes Homo floresiensis our distant cousin, not our ancestor.

Why would even experienced science reporting portals such as National Public Radio keep calling the Hobbit as our ancestor? Here are some examples from their article:

"Some scientists have said the Hobbit, found in Indonesia, is a weird human ancestor that somehow survived until some 12,000 to 20,000 years ago....."

"Regardless of whether the Hobbits are our ancestors or simply abnormal humans, they clearly defied steep odds to survive".

I think it has to do with the primitive traits shown by the Hobbit. Primitive traits are those aspects of our morphology or behavior that we inherit from our ancestors and are conserved, i.e. are not changed much. The Hobbit in aspects of its skull morphology and now the shape of wrist bones has retained and conserved traits that it inherited from its early Homo erectus ancestors in east Africa. Some time after the ancestors of the Hobbit had left Africa, evolution changed the shape of the wrist bones in some populations of erectus in Africa. This new wrist bone shape is said to be a derived trait with respect to early Homo. Populations carrying this derived wrist bone shape can be thought of as the common ancestor of the Neanderthals and modern humans. One such population migrated to Europe and evolved into the Neanderthals. Another population evolved into modern humans in Africa.

Hominids who carry ancestral or primitive traits are not necessarily our ancestors. Evolution is a branching process. An ancestral trait may be conserved during evolution in descendants of one branch of the family and modified by evolution in descendants of some other branch. The wrist bones in the human family illustrates this concept very well.

Tuesday, September 25, 2007

Part 5 of the six part series on Pune city pollution and environment. Updated every Tuesday.

In this blog I integrate geology and high-resolution images with GIS, to showcase some example of poor urban planning and cases of violation of the urban development plan in Pune. The list of violations of building codes in Indian cities will be quite long. In recent months controversies over whether to build on the hills, and flooding of premises built too close to streams and rivers have caught the public attention. I have highlighted these types of violations since they require some geological knowledge and image interpretation skills to spot. At the end I will discuss some limitations of this approach.

Hill Top Hill Slopes:Hills are measured in terms of gradient, which is merely the rise of the hill over the run. If you're going up 2 feet for every 100 feet you travel, you're on a 2% hill. For the purposes of urban zoning, the Pune Municipal Corporation Development Plan defines any hill slope with a gradient of 20% i.e. 11 deg or more as falling within a Hill Slope/Hill Top zone (HS/HT). According to the development control rules, owners of plots in HS/HT zones can have a built up area up to 4% of the plot area. Recently, all HS/HT were given protected status and all construction halted.

Construction on steep hill slopes can occur under a number of circumstances.

1) The slope was constructed upon at a time when the area fell outside the limits of the development control rules, i.e. outside PMC limits. This is a common situation in the fringe villages which only recently came under PMC jurisdiction.

2) The slope falls under HS/HT zone and has been encroached upon by slums. This situation is common for HS/HT zones under government ownership.

3) The slope falls under HS/HT zone and constructions have come up as per the development restrictions defined for HS/HT.

4) The slope is reclassified as not falling under HS/HT. Constructions on such misclassified slopes follow normal development control rules. This is a particularly insidious form of corruption of the urban development plan, since the "reclassification" allows plot owners to bypass the 4% rule and construct mansions on hills. Image below depicts this situation.

The green line is the gentler slope. The yellow line is the steep rocky slope (HS/HT). The orange dotted lines outline a layer of black basalt rock. This layer can be traced from the upper left of the photo where it lies in the HS/HT reserved forest of Vetal Tekdi, along the entire length of the base of Chaturshringi hill. Since the basalt outcrop is horizontal the upper and lower dotted lines are analogous to contour lines. The gradient between them is the same along its entire length and should fall under the HS/HT zone along its entire length. On the lower right however one can observe massive constructions intersecting the basalt layer. The gradient at the site of these construction has been "reclassified" to residential to allow owners to maximize FSI (floor space index).

Encroachments of river banks:During the recent monsoons, Ram Nadi, a tributary of the Mula river flooded its banks. Water entered the premises of several constructions built close to the banks. Residents, city government and the media suddenly woke up to the fact that these houses were built with scant regard to urban development rules, which mandate a no construction zone of 30 metres near water bodies. Below is an example of a clear violation of that rule. Image shows a section of the Mutha river near the bridge connecting Karvenagar and Sinhagad road.

I have built a 30 metre buffer along the river banks (green band). River banks are the blue lines. Flow is from right to left. On the south bank (top of image) one can clearly see big apartment complexes falling within the 30 metre buffer. Red arrows outline the unnatural right angle the river bank takes, which means that the river bed has been encroached upon by dumping massive amounts of debris.

Blockage of natural drainage:Hill slopes have natural drainage made up of small streams. A proper urban development plan should take into account such drainage and not allow constructions to block these streams. However, natural drainage everywhere in Pune has been built upon, simply by filling up these streams. Since during monsoons, water does not find a natural drain, this results in sheet flow of water onto the roads. The erosive power of this water is quite significant, resulting in the famous pot-holes of Pune. Below is an example of natural drainage which has been blocked by several constructions.Source: Google Earth ; Image Copyright: 2007 Digitalglobe ; 2007 Europa Technologies; 2005 Google

Flow of streams is from left to the right of the image. If one follows the red arrows, you can make out the curvilinear outlines of a small stream which at places abruptly terminates against buildings. This stream joins another stream outlined with blue arrows and forms a bigger drain at the purple arrow. This then flows into the Mutha river. Such blocked streams have only recently caught the attention of the city government, which has promised to amend building rules to allow natural passage of this drainage.

Some technologies such as Google earth allows citizens to locate violations of the urban plan. One can use the distance tools to measure and also draw outlines of objects and save them in a geographic format. These files can be shared with other Google earth users. In this way, citizens can participate in discussions and debates on urban planning without needing expensive GIS software. They can also register complaints with the Municipal Corporation online. But the images are not really a monitoring tool. The images are 6 months to 3 years old. The city government however can use remote sensing as a monitoring tool, if they decide on purchasing high-resolution images every 3 months or so. A one meter resolution image covering Pune municipal limits should cost about Rs. 3-4 lacs. So a purchase budget of Rs. 12-15 lacs a year will give the municipality a powerful urban planning tool not just for spotting violations but also for other urban planning purposes. This off course has to be accompanied by a dedicated GIS staff, in which the city government has shown little inclination and interest.

Saturday, September 22, 2007

Read an interesting piece of research by Stanford University researchers on why humans live well beyond their reproductive years. I first read it in Science Daily, but here is the original press release from Stanford University. Organisms that cannot reproduce are irrelevant evolutionarily. So natural selection should ideally design the human life cycle to cease once our reproductive years are over. But women live well beyond menopause into their 70's and 80's. One explanation is that women need to live long enough to raise kids in to their independent years. But this could raise longevity to the 60's at most. Another explanation is the "grandmother hypothesis" which suggests that old women by helping raise grandchildren successfully, will pass genes for longevity through their grand kids, so over time increasing longevity beyond menopause. Both these theories are plausible, and the Stanford researchers have added another.

They look at male reproductive biology. Unlike women, men do not have their fertility suddenly cut off at menopause. Rather it declines gradually. But if a man's life partner hits menopause, then shenanigans aside, the man also becomes evolutionarily irrelevant and should face death. However, since most men marry younger women, this irrelevance is postponed to later years, and if older men take very young wives, then it may be postponed almost indefinitely. So, because over human history, very old men have taken very young wives, genes that cause harmful mutations later in life have been steadily winnowed out by natural selection and genes for longevity have accumulated. Because over evolutionary time, a gene spends roughly half its time in women, their longevity has increased as well.

All of this very interesting, except starting from the Stanford press release, all news organizations describe this as an example of evolution as good for the species!

"It turns out that older men chasing younger women contributes to human longevity and the survival of the species" - states the Stanford press release

and

"But the fatherhood of a small number of older men is enough to postpone the date with death because natural selection fights life-shortening mutations until the species is finished reproducing". (this off course should be "until the individual has finished reproducing", but it shows how deeply embedded is our thinking that species is what matters in evolution).

The emphasis on the term species is mine. This is an old fault in our thinking to visualize individuals as striving for the benefit of the species. Humans and all organisms behave in ways that increase their own chances of survival and reproduction. That behavior may have an effect that has some benefits for the larger group, but that does not mean individuals are behaving for the benefit of the larger group. What would our reproductive behavior be if we were acting for the benefit of the species and not for ourselves? For one, evolution would have led to behavior that strictly imposed a limit on the number of offspring, an evolutionarily imposed population control. That does not seem to be the case. Secondly, since the quality of gametes decreases with increasing age, we should have evolved behavior that imposed a limit on the age that we reproduce. But men especially seem to retain fertility until a very old age.

Surprising that a University as renowned as Stanford will make such mistakes, but it shows how little control scientists have over even their own organization's press offices. The good of the species theme appeared in Times of India too. Besides that mistake, Times of India missed out on something else. One of the lead researchers from the Stanford group involved in this work is an Indian, ShripadTuljapurkar. Our media missed out on a big opportunity to do some major chest beating :)

Tuesday, September 18, 2007

Part 4 of the six part series on Pune city pollution and environment. Updated every Tuesday.

Tropical forests are extremely important to the global carbon cycle. These forests remove a high proportion of carbon dioxide being emitted by industries and through deforestation. Human activities emit around 25 billion tons of carbon dioxide (CO2) every year. Out of that about 30% is absorbed by the oceans, about 40% stays in the atmosphere and about 30% is thought to be absorbed by forests. Temperate forests are less efficient in sucking in CO2 as compared with tropical forests. But the amount of forest cover is steadily decreasing thus increasing the amount of CO2 that stays in the atmosphere. Deforestation is the second biggest emitter of CO2 after power generation as can be seen in the figure below on greenhouse gas emissions by source (source: World Resources Institute).

In general mature forests are not net absorbers of CO2, since they give up almost as much CO2 through rotting biomass. New growth forests are more efficient absorbers of CO2. So planting trees and expanding forest cover rather than just maintaining forests will lead to offsetting of CO2 emissions.

Right on! Trees as life givers of oxygen (I often wonder why people don't choke to death in deserts), trees as the lungs of our city, save trees and breathe better, all these have become popular slogans. Here are a few more from Pune environmentalists:

"..these green areas give Oxygen....(for us humans..and this is the only source of Oxygen on the planet), help to reduce pollution, and preserve our eco-environment" in this article

and recently (Times of India, Sept 13 07, Pune) by noted environmentalist Anita GokhaleBenninger" An average Pune family size of five people will require 60 sq metres of green areas to breathe and survive. Once preserved and re-forested, the PuneBDP (biodiversity parks) will provide clean air for approximately 35 lakh (3.5 million) people living in this area"

The ability of trees to absorb CO2 has lead to an unquestioned faith in their ability to provide us with clean air. But can trees provide us with that service?

Let's take pollutants that harm us now, and pollutants that will harm us in the future.

Vehicles in Pune emit several hundred to thousands of tons of harmful pollutants like SOx, NOx, HC and PM10 (particulate matter) every year. These are having immediate health effects on citizens. But trees do not absorb these chemicals. No amount of tree plantations will have any effect on the amounts of these pollutants in the air. Ultimately only better quality fuel and to a certain extent a better public transport system will have any appreciable impact on Pune air quality. But trees also absorb dust. Won't that reduce for example the amounts of particulate matter. Ms. Benninger recently calculated that trees in the proposed biodiversity parks will trap around 80 thousand tons of dust per year. The problem is that a large proportion of particulate matter that harms citizens is adsorbed on dust lying of unclean and unpaved roads. Pune Municipal Corporation Env. Status report 2006-07 indicates that nearly 6 thousand tons of particulate matter adsorbed on dusty roads get suspended by vehicular traffic. This is the dust that harms citizens health. The solution for this problem is not trees on hills but better paved roads which are cleaned regularly.

And what about pollutants like CO2, which through its effect on global warming will harm us in the near future? Is the tree cover in Pune offsetting sufficient amounts of CO2 emitted from vehicles? The discrepancy is startling. Here are two examples:

The forest cover on Law College Hill and VetalTekdi absorbs about 1.5 tons of CO2 per year. In contrast, idling your vehicle for 5 minutes at Nal Stop every day, will lead to emission of about 625 tons of CO2 per year (amount calculated for total number of vehicles passing through Nal Stop every year).

The total amount of CO2 absorbed by the tree cover in Pune is about 55 thousand tons per year. In contrast, vehicles emit about 2 million tons of CO2 per year.

So Pune tree cover cannot save us from the increasing amount of CO2 emissions either. Increased plantations especially on the hills will help increase the amounts of CO2 absorbed, but I feel they will play no significant role in offsetting vehicular emissions.

Image below shows managed forest on Pune hills.

The second topic I want to briefly touch on is the reporting on the proposed biodiversity parks on the hills. There are complex legal issues involved in this since the ownership of the hills is split between the forest department, the government and private land owners. A significant portions of the hills have been encroached upon by slums. Recently from an environmental perspective the reporting has focused upon carbon trading schemes and whether they can generate funds for land acquisition. The basic idea is to use plantations on Pune hills to offset CO2 emissions and get paid for every ton of CO2 absorbed. Supporters of this scheme say that significant amounts of funds can be generated by plantations on Pune hills. Here is a summary of a recent calculation by Ms. Benninger (Times of India, Sept 13, 07, Pune):

The amount of hill land is 1646.74 hectares. Each forest hectare will absorb around 55 tons of carbon per year. Therefore the total amount of carbon absorbed per year will be 90,530 tons. Carbon credits are presently sold for around $12 per ton of CO2 eq. (my link) and will increase in the near future. So amount of funds generated per year will be around 4.88 crore.

First some technicalities. Some of the hill land is already built upon legally and will in reality never be available for any plantations. Further, is it 55 tons of carbon or carbon dioxide? If it is carbon that means almost 200 tons of CO2 will be absorbed per forest hectare per year (one ton Carbon combines with oxygen to give 3.62 tons CO2). Either way, 55 tons absorption of carbon or carbon dioxide is a gross exaggeration (doesn't the media ever do any background checks?). Amount of CO2 absorbed per forest hectare varies depending on the climate (temperate or tropical) , soil quality, and species of trees. Generally the range is from about 6 tons per year for temperate areas to anywhere from 5 tons to 20 tons per year for tropical areas.

All these amounts are for managed plantations. Currently our forest on various hills (few hundred hectares) are absorbing in totality around 3-4 tons of CO2 per year. This is an abysmally low figure but not very surprising if you are to walk on these hills. The vegetation is stunted and sparse. It sheds leaves starting December and lies bare until the monsoons. By February the forest department starts burning the underbrush as part of their forest management plan. This means emissions of CO2. I doubt if there is any net absorption of CO2 by these forests, especially in the more mature stands. Considering the rocky soils of the hills, no amounts of additional plantations will raise CO2 absorption to a quantity that can generate any significant funds. Besides, environmentalists agree that even the dubious 4.88 crore per year they have calculated is too little an amount for land acquisition, which will require according to estimates several 100 crores.

On this funding issue, the Maharashtra government has been disingenuous. They have transferred the burden of coming up with the funds for the biodiversity parks onto the Pune Municipal Corporation and are refusing to pass the green development plan for the city, which has earmarked the hill areas as biodiversity zones. However, large amounts of money which will unlock land on the hills especially through slum rehabilitation is tied to the Jawaharlal Nehru National Urban Renewal Mission, a central government scheme to modernize Indian cities. The centre will not release that money to the Maharashtra government until they repel the Urban Land Ceiling Act , which the Maharashtra government is hesitating to do. That really should be the thrust of the arguments made by the PMC and environmentalists in the effort to acquire land for the biodiversity parks.

In summary, regarding the biodiversity parks, I feel carbon trading schemes will not generate any appreciable funds. Besides, the very nature of carbon trading schemes through plantations is incompatible with what should be the real goal of the biodiversity parks, which is maintaining and expanding biodiversity. Trading schemes require that plantations consist of rapidly growing trees. Even though indigenous species will be preferred, it would inevitably mean that the plantations will consist of only one or two rapidly growing indigenous tree species, defeating the purpose of developing and maintaining biodiversity.

Trees on Pune hills will not provide citizens with clean air nor will they significantly offset CO2 emissions. The real value of urban forests on these hills is that they provide citizens with open recreational areas, and if properly developed will create expanded habitats for land animal and bird species, thus genuinely contributing to rich urban biodiversity. That by itself is a goal worth fighting for.

Sunday, September 16, 2007

By now everyone has had saturation coverage of this issue. For those still uninitiated, Ram Sethu refers to a hypothetical man-made causeway bridging the Palk Strait between India and Sri Lanka. Because it is believed to have been built by Sri Ram on his way to Sri Lanka, a recent report by the Archaeological Survey of India, stating that the Ram Sethu is a natural formation and that there is no scientific evidence of the existence of Ram has ignited a controversy. Sensing a popular backlash, the government in an act of gross cowardice have censored the scientists, whose job was to present scientific evidence and which they did. These issues have been dealt with here and here. Since my interest is in science I will write about that. I have watched with increasing disbelief over the gross ignorance shown by media and various "experts" over the validity, reliability and appropriateness of the different scientific tools that are being used to assess the status of Ram Sethu. So I have compiled a dummies guide to Ram Sethu, which points out the various misunderstandings and misinterpretations of scientific techniques and data.

Both conclusions drawn on the basis of satellite data are wrong. 1a) The satellite image do show natural sand shoals and coral islands. But the images being used to draw this conclusion cannot resolve features that lie on the sea bed. There could well be artificial structures that cannot be seen in the images. 1b) The continuity of the linear feature seen in the satellite images is an illusion caused by suspension of calcium carbonate sediment and cloud cover. Seen from great altitude this appears to be continuous. Close up of the Palk Strait show a discontinuous series of islands. In short, the commonly shown satellite images due to their poor spatial resolution and their inability to penetrate through water (spectral resolution) cannot be used to make any inferences about what lies on the sea-bed.

2a) NASA scientists say that Ram Sethu is a natural feature. 2b) NASA scientists have left the question open to interpretation, so there could be an artificial struture.

NASA scientists have never been to the Palk Strait and looked at the undersea geology themselves. Why this obsession with NASA scientists? Why not discuss geological research done by Indian scientists, who have actually done field work in the Palk Strait.

3) The Ram Sethu is millions of years old. So there cannot be an artificial structure in the Palk Strait.

Again a wrong conclusion from a partially correct statement. The rock formations and sediments in the Palk Strait were deposited over millions of years at least from the Miocene to the present. No matter how old some the rocks are, there still could have been a recent construction of some sort, using these old rocks as building material.

4) The sand in the Palk strait is just 3500 years old. This supports the idea that the Ram Sethu was constructed by Sri Ram.

Wrong conclusion from possibly correct data. Many of the sand shoals are of Holocene age. But this is unconsolidated sand, which has been brought in by currents from the southern Tamil Nadu and Jaffna coastlines to form natural sand islands. The correlation of age between these sands and the purported age of the Ramayan is purely coincidental.

5) Carbon dating has shown the Ram Sethu to be a lakh or few lakh years old.

Carbon dating uses the amount and natural decay rate of C14, an isotope of carbon to calculate the date of artifacts and other organic materials. It cannot be used to date organic materials older than around 40 thousand years. This is because the half life of C14 (time required for the quantity to decay to half of its initial value) is about 5700 years, and in about 8 half-lives the amount of C14 left in the material is too little to measure accurately.

6) Geological cores have shown the presence of boulders on top of sand in the vicinity of coral islands in the Palk Strait. The boulders could not have appeared on top of sands by any natural process. So they are man-made features, part of an ancient causeway.

Again an astonishingly ignorant statement by a senior geologist. I have posted a detailed criticism of this, describing how natural processes can easily explain the presence of boulders on the sea floor.

7) Some of boulders of coral rock are light enough to have floated on the water.

As ignorant as it gets. What pray tell us , then are the boulders doing on the sea-floor? Coral rock is made up of calcite and aragonite, minerals with a specific gravity of 2.71, much more than water.

8) The causeway was built during a period of sea-level fall a few thousand years ago when much of the Palk strait sea bed was exposed.

Again not possible. Holocene sea-level falls as shown by coral reef terraces (bands of corals growing at different heights) were not big enough to have lowered sea-level to any appreciable extent.

9) The Ramayan is 1.7 million years old. An absurd statement. Humans did not exist at that time. I will not dwell on this, as it has been covered by this excellent blog.

10) The Ramayan is 9000 B.C, 7000 B.C, 5000 B.C. take your pick.

I listen and read in amazement when dates are thrown recklessly and with full confidence by historians and scientists alike (Time of India Sept. 14 '07 quoted eminent anthropologists given dates as old as 5000-6000 B.C.) without a murmur of dissent or criticism by our media. All these dates are too old. All three dates take us back to the stone age. The metal age in the Indian subcontinent began around 4000-3500 B.C. The Ramayan judging by the descriptions takes place in the iron age, which began in the Indian subcontinent around 1800-1500 B.C. The totality of the archaeological and linguistic evidence suggest that the Gangetic plain societies which the Ramayan describes arose starting around 1000 B.C.

I have observed in particular the careless use of dates to support either the natural formation or man-made point of view. As I have described above the dates of the rocks and sediments do not by themselves inform us on whether there is an artificial causeway. But there are two types of information about dates of the rocks that are extremely important, the significance of which have escaped the media and scientists alike. The first is the dates of the coral terraces at Rameshwaram island. The oldest coral terrace is about 5400 years old. The second terrace about 10-15 cms below is about 3900 years old. Some distance away at Mandapam the upper terrace shows an age of 3600 years ago and just 20 cm below that one gives an age of 2630 yrs. Do coral terraces reflect oscillations of sea level or do they simply reflect that loci of coral growth shifted over time due to local changes in water quality, sediment disturbance and nutrient availability? As yet there does not seem to be field evidence that shows exposure surfaces between these terraces which would be an indicator that sea-level fell, exposed large areas and then rose and drowned the area again, forming the younger terraces. Such an exposure surface will provide a reliable data to the sea -level fall. At present all we can say with any confidence is that sea -level fell after 2600 years B.P. Holocene sea-level fluctuations did take place but they were likely not extensive enough to expose the Palk Strait sea bed over most of the basin as happened in the Pleistocene. The second situation regarding dates is hypothetical but presents an interesting situation. Suppose an artificial structure is found on the sea floor, but the dates of the boulders indicate that the boulders are just few hundred years old. What would supporters of Ram's bridge say then?

If readers have any other nuggets of inane statements by media and experts please let me know and I will write another installment.

Wednesday, September 12, 2007

Alex, an African grey parrot and one of the most celebrated scientific subjects died of natural causes a few days ago. He was 31 and spent most of his life working with Dr. Irene Pepperberg, a comparative psychologist at Brandeis University and Harvard. Alex became famous for his cognitive abilities. He knew more than 100 English words, could tell between different colors and shapes and occasionally came up with unique one-liners which would amaze people not familiar with success rates of animals trying to "speak". Alex's considerable abilities, along with other examples of studies of birds, are making us aware that birds are not ...well....bird-brained.

For example some recent studies on Caledonian crows have revealed complex tool manipulation abilities in those crows. These birds show the ability to use one tool to manipulate another tool to achieve a particular task. In one study, food was stored in a hole out of reach of an easily available, but short stick. A long stick which could reach the food was kept some distance away in a toolbox. The crows quickly learnt to use the short stick to fish out the long stick from the box and then use the long stick to get at the food in the hole. In a variation of this study, researchers reversed the position of the sticks. The crows again quickly modified their behavior and directly used the long stick to get at the food.

In another interesting piece of research on scrub jay's, researchers noticed that scrub jay's bury their food from rivals and then surprisingly some scrub jay's sneak back and re-bury their food when their rivals are not present. This was seemingly being done to avoid pilfering by other birds. The shock came when controlled experiments revealed that only those scrub jays who themselves had previously stolen other scrub jay's food came back to relocate their food resources. Jay's with no previous experience of thieving did not bother re-burying their food. All this suggests that these birds have some sort of a ' theory of mind' i.e. the ability to use one's own experience to mentally time-travel and anticipate the actions of another and then use that information for manipulative purposes. This ability to sense that other individuals have thoughts and desires similar to yours was thought to be restricted only to humans, but evolution seems to have given rise to analogous abilities in some species of birds as well.

Alex's passing has generated a fair bit of press. Eulogies have ranged from the decent and serious as in this NYtimes report, to the light-hearted as in this blog. This leaves some space for dark comedy, an opportunity I don't want to miss. So in the words of Monty Python's enraged customer who tries to convince the pet-store owner that the parrot he bought from him an hour ago is really dead, a somewhat macabre goodbye to Alex:

''E's passed on! This parrot is no more! He has ceased to be! 'E's expired and gone to meet 'is maker! This is a late parrot. 'E's a stiff! Bereft of life, 'e rests in peace! If you hadn't nailed 'ime'd be pushing up the daisies! 'Is metabolic processes are now 'istory! 'E's off the twig! ' E's kicked the bucket, 'e's shuffled off 'is mortal coil, run down the curtain and joined the bleedin' choir invisibile!! This is an ex-parrot.

Tuesday, September 11, 2007

Part 3 of a six part series on Pune city pollution and environment. Updated every Tuesday.

Didn't you see my right foot?! In the middle of an argument over a minor accident the rickshaw driver claimed he had poked his right foot out to indicate that he was turning right. Pune has around 60-70 thousand three wheeler rickshaws. They are no doubt a very convenient form of taxi service. To many harried customers, rickshaw drivers are rude and indisciplined, but I don't really find their behavior on the road to be any different than that of private vehicle owners. This is a country where everyone owns a piece of the road, so rules be damned.

But rickshaws do pollute a lot. Below table shows pollution amounts in tons/year for different pollutants for a total of 62, 600 rickshaws, compared with other vehicle types. Source: Emission factors from S. Guttikunda, World Bank. Rickshaw numbers from N. Iyer, Consultant Bajaj Auto. Values represent combined sum for two stroke and four stroke rickshaws. Other vehicle numbers, from Pune Municipal Corporation, Env. Status report 2005.

As I showed in my previous post, buses pollute more on an absolute basis but are more fuel efficient on a per passenger km basis. What about rickshaws? Below graph shows per passenger km pollution for a trip of 100 kms. It shows that rickshaws pollute more than buses and two wheelers on a per passenger km basis.

To tackle rickshaw pollution, the Road Transport Authority has made a policy decision to convert existing 2 stroke and 4 stroke petrol rickshaws to natural gas powered vehicles. How much reductions in emissions will be achieved by conversion of petrol rickshaws to CNG? (compressed natural gas). Below table shows reduction in emissions in tons/year for rickshaw and for comparison reduction in emission for PMT buses.

Blank fields indicate lack of data for emission factors. However, SOx emissions are expected to decrease by large amounts for CNG rickshaws.

A conversion of existing fleet of 2 stroke and 4 stroke rickshaws to CNG has the potential to reduce CO and HC emissions by around 95 percent and PM emissions by around 40 percent! There would be significant reduction in CO2 (by about 30,000 ton/yr, or about 20%). Public transport contributes to a substantial portion of total vehicular pollution. My admittedly rough estimates suggest that public transport including rickshaw, PMT buses and private company buses (about 8000 of them according to the municipal corporation) contribute about 40% of total SOx emissions, 30% of PM10 emissions and about 35% of CO2 emissions. Conversion to cleaner fuels will definitely lead to improvements in air quality, especially if the several thousand private company buses are also included. But changing fuel quality of public transport alone may not help in the long run. In Delhi, after significant improvements in air quality due to conversion of public transport to CNG, the latest news is that pollution is on the rise again, due to a heavy influx of private vehicles, many of them running on diesel. Pune faces similar problems with about 6000 new vehicles being registered every month. And with the eminent arrival of the much touted 1 lakh rupee car in the next few years, gains in reducing emissions by cleaner fuels in public transport vehicles may be swamped by the enormous increase in private vehicles. A more comprehensive public transport system needs to be pursued with urgency combined with pricing initiatives to make driving private vehicles more expensive.

Finally some thoughts on six seater rickshaws, those horrendous contraptions, which were banished to the outskirts of the city, because they were thought to be "polluting more". Image shows a six seater in Pune suburbs.I have to admit I have a liking for these beasts. There is no doubt that they offered frequent and cheap transport services, something that the bus transport has failed to offer. In principle they should not pollute more than rickshaws, maybe even less on a per passenger basis, since on average they carry more passengers. But a widespread use of adulterated fuel and very poor engine maintenance has lead to additional pollution. Here's a thought. Why doesn't the PMT offer their own six seater service? Is it necessary that they offer only a bus service? This way at least the fuel quality can be regulated, and drivers can be trained to obey at least a few rules.

Notice the similarity? The first set is from the Florida Flambeau, the campus newspaper of Florida State University, Tallahassee, and the second is from the Times of India, one of the leading english-language newspapers in India. Apart from self absorbed campus newspapers, the only situation when most science news portals reveal the nationality of scientists in a headline is when prestigious awards such as the Nobel are announced. These two headlines reveal a little of the ways Indians think. The first one (IITM means Indian Institute of Tropical Meteorology) shows the sometimes unhealthy and exaggerated respect for seniority and labels that is now deeply embedded in our way of thinking. The nobel prize winning scientist must be right. So, for a Indian scientist to question this great achiever has to be something revolutionary. I read through the report. There was nothing that extraordinary about the research. It was one of the countless questions being raised over the importance of aerosols on global warming. The second headline (NRI means non resident Indian) is all about our obsession with staking a claim over anything Indian, however tenuous the connection. The huge outpouring of pride over astronaut Sunita Williams achievements, a first generation American with ancestral ties to India is another good example.

Science news need not be expressed in such nationalistic terms. Reporting the actual science frequently and accurately will be inspiring enough.

Tuesday, September 4, 2007

Part 2 of a six part series on Pune City pollution and environment. Updated every Tuesday.

New Delhi, Asian Games 1982. I have memories of broad, clean avenues and clean air. When I returned after a long gap in 1999, New Delhi was urban hell. My friend pointed out a particularly busy intersection and said, "that's the most polluted intersection in Asia". I went back in 2004, and something strange had happened. Something we Indians are not used to. Pollution had reduced dramatically. Air quality was better. The reason experts tell us, was the conversion of almost the entire public transport fleet (15-20 thousand vehicles by various estimates) of rickshaws, taxis and buses from diesel to CNG (Edit: Compressed Natural Gas).

How much will Pune Municipal Transport (PMT) benefit from a conversion from Diesel to CNG? Graph below shows the potential in reducing emissions (tons/year) by converting the current Pune Bus Fleet of 990 buses (PMT plus rental) from Diesel to CNG. (for the purpose of the calculation I have assumed all 990 buses are on the road everyday, which given the state of disrepair of PMT buses may not be the case).

A CNG fleet will lower emissions of PM10 (particulate matter) from 135 tons/year to about 40 tons/year (70% reduction), of SOx from 80 tons/yr to about 25 tons/yr (68% reduction) and CO2 from about 65 thousand tons/yr to about 35 thousand tons/yr (46% reduction). There are considerable (about 50%) reductions in nitrogen compounds as well, but I did not have the emission factors available to make any specific calculations. But what about methane? CNG is about 80% methane, which is 20 times more potent a greenhouse gas than CO2. Won't the higher methane emissions offset the lower CO2 emissions? Apparently if one considers the total fuel cycles of diesel and CNG including emissions during fuel production, CNG buses have total greenhouse gas emissions similar to diesel buses. Diesel also emits toxic compounds like polyaromatic hydrocarbons, benzene and 1,3 butadiene that CNG does not.

How does bus pollution compare with other vehicles? Although Diesel or CNG buses may emit more pollutants than a 2 wheeler or car in an absolute sense, are they at least more efficient on a per passenger km basis considering they carry more passengers per trip? Graph below shows the emission of pollutants per passenger km, if a commuter makes a daily trip of 30 kms to and from work. The calculations show that even on a per passenger km basis Diesel buses emit more particulate matter than 2 wheelers. CNG however on a passenger km basis is much cleaner than petrol and diesel vehicles.

To summarize, conversion of PMT buses to CNG will definitely benefit the city. An even bigger reduction in emissions would be achieved through the conversion of several thousand private buses. There is a move to convert the fleet of rickshaws to LPG/CNG. More on that in another blog.

As fuel costs keep increasing, public transport will increasingly be the more cost effective means of transport. Below graph shows Per Km Petrol Cost for Two Wheelers vs Bus Fare Cost per passenger km

Source: Central Institute of Road Transport

The trend indicates that due to increase in petrol prices, public transport per passenger km is increasingly a more efficient mode of transport than private vehicles.

Be sure to read about CNG facts and myths in this fact sheet from the Centre for Science and Environment in Delhi and also about CNG buses and how they compare with Diesel in this fact sheet from the U.S. Dept. Of Energy.

Saturday, September 1, 2007

A short article appeared in NewScientist online on archaeans, a microbe with a prokaryotic cell similar to bacteria. Apparently in the varieties of archaeans on which this particular research was carried out, it was not possible to categorize them into separate species, due to extensive lateral gene transfer i.e. varieties of archaeans were swapping genes between them to an extent that they were not genetically distinct enough to be called separate species.

What are species? The term is so commonly used that it comes as a surprise to learn that this has been a vexing question for biologists to answer. Species are interbreeding aggregates of populations that are reproductively isolated from other such groups due to physiological or behavioral barriers. In asexual organisms this definition runs into an obvious problem which is that these organisms do not interbreed, they are clones. Species in these cases are recognized on the basis of ecological preference and or morphological differences. Extinct organisms pose another problem. Here, the recognition of fossil species is on the basis of morphological differences, the rationale being that if populations show enough morphological differences then individuals belonging to these different populations would not or could not have interbred. But how much difference is enough? The literature on species concepts is large. I found Keywords in Evolutionary Biology to be one of the best reference books. Recently, this blog raises interesting questions on the concept of species.

Okay, on to Archaea. The article in NewScientist begins with the sentence:

"Some primitive organisms may be impossible to divide into species".

Are Archaea primitive? Primitive as in early inhabitants of earth, or primitive as in "less evolved"? To paraphrase Bill Clinton, it depends on what the meaning of the word "primitive" is is. Below is the phylogeny of life (source: Wikipedia)

Bacteria, Archaea and Eucaryota (the group we belong to) form three major domains of life. These three domains have had more or less the same time to evolve since their descent from the universal common ancestor. Some biologists have argued in favor of a different phylogeny, one in which Archaea and Eucaryotes evolve from a variety of bacteria, but you get the point. To say one living group of organisms is more primitive as in "less evolved" than any other is meaningless. It is not as if Archaea originated early in the history of life and stopped evolving. All organisms have primitive and derived traits, i.e. some properties which were inherited from their ancestors and conserved or were not changed much, and derived properties that arose later in the history of that lineage. So, for example certain aspects of cell physiology in humans is regulated by molecular mechanisms that are nearly identical with other vertebrates. This is a primitive trait, that must have arisen in the common ancestor of vertebrates and has not changed much since. Other properties such as our bipedal gait evolved uniquely in our lineage later. This is a derived trait. Archaeans must also contain such primitive traits that they inherited from ancient archaeans and some derived traits which must have evolved more recently.

Biologists have long since discarded the concept of scala naturae, the linear arrangement of life forms from the lowest presumably bacteria, to the highest- us humans. But in popular imagination, we remain bound to this great chain of being.

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ABOUT THIS BLOG

I am a Sedimentary Geologist. On Rapid Uplift I write mostly about topics within the geosciences, but sometimes on biological evolution and environmental issues. I like to travel and in my free time I teach 12 year old kids soccer and rugby.